[gmx-users] Help with simulation

Jodi Fangman jodi-fangman at uiowa.edu
Fri Nov 14 16:01:01 CET 2003

I am a relatively new gromacs user and have run into a problem. I am trying to 
simulate a small protein in solution to examine side-chain rotomer 
distributions. I have been able to run the simulation in water but would like 
to run it with ions as well. I was able to add the number of ions I wanted 
using genion without any problems. I then changed my *.top file to the new 
number of waters and added the ions. I also added the ions.itp reference in 
this file. When I try to run the simulation with the ions included I receive an 
error message. The error message says: FATAL ERROR no such atomtype 'K'. This 
is the error I receive whether I am using potassium or sodium as my positive 
ion. I can not figure out what is going wrong. Have I miss entered/referenced 
something? Will my forcefield not recognize ions? (I am using the GROMACS 
forcefield with all hydrogens) Or is there a different problem that I am not 
aware of? Thank you for any help you can provide.

Jodi Fangman
Jodi Fangman
Robertson Lab
University of Iowa
51 Newton Rd, 4-403 BSB
Iowa City, IA 52242
Ph: (319)335-6516

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